Tree Position

R-P312/S116 > Z40481 > ZZ11 > DF27/S250 > Z195/S355 > Z198 > Z46513 > ZS312 > Z262 > M167 > Z264 > Z205 > ~22224168-A-C > Z206/S235 > BY3222 > Z29719

Unique Mutations

The mutations unique to this man are summarized in the table below. Those with a '+' or '*' confidence level are considered by FamilyTreeDNA or FullGenomesCorp to be high quality SNPs/INDELs. For completeness, all other mutations of lesser confidence are included as well. These additional mutations may be useful for distinguishing between very closely related men.

Occasionally, some of the mutations listed here will be thought to be shared with other men in which case they might appear in upstream blocks on the tree. When this happens, the 'Blocks' field will indicate what block they appear in. Such a situation might arise with BigY men if the BED data suggests another man may be positive for a SNP, even though it doesn't appear in his VCF data. It might also happen if Chromo2 testing or Sanger sequencing of other men not on the tree show the SNP to be shared.

POS-REF-ALT (hg19) POS-REF-ALT (hg38) Blocks Names Region McDonald BED combBED STR1kG
2807063-TAA-T 2939022-TAA-T +
22295984-C-T 20134098-C-T DYZ19 +
18246092-CGT-C 16134212-CGT-C +
9231625-T-C 9394016-T-C Y+
6744283-T-G 6876242-T-G CTS422 YY+
6826955-T-C 6958914-T-C Z10163 Y+
8485953-C-T 8617912-C-T FT300452 YY+
8844035-G-C 8975994-G-C BY76296 YY+
14109062-C-A 11988356-C-A PH917 BY12862 Z40986 YY+
14203314-C-T 12082608-C-T BY93832 YY+
15001224-T-C 12889309-T-C PH1559 YY+
15519186-C-A 13407306-C-A PH1737 YY+
16494418-T-G 14382538-T-G F20751 YY+
16740178-C-G 14628298-C-G PH2485 YY+
17066342-T-C 14954462-T-C FT301542 Y+
17082507-G-A 14970627-G-A CTS6732 YY+
17613352-T-C 15501472-T-C FT301680 YY+
18100931-G-T 15989051-G-T FT105607 YY+
18145172-G-T 16033292-G-T PH3718 YY+
18564785-C-T 16452905-C-T PH3832 YY+
18601690-G-T 16489810-G-T PH3859 YY+
18902173-A-C 16790293-A-C FT302012 YY+
18986742-G-T 16874862-G-T PH4133 YY+
19215057-G-T 17103177-G-T YY+
21405555-G-T 19243669-G-T PH4805 YY+
21870479-T-G 19708593-T-G PH4991 YY+
22668596-C-G 20506710-C-G Y+
23093447-A-G 20931561-A-G FT302805 Y+
23244078-C-T 21082192-C-T BY4392 YY+
2810389-T-TTTG 2942348-T-TTTG +
3101382-T-C 3233341-T-C FT103540 +
3115733-C-T 3247692-C-T FT47092 +
3571635-C-CT 3703594-C-CT +
3640728-CCTT-C 3772687-CCTT-C +
3837725-A-C 3969684-A-C FT318660 +
3916954-AT-A 4048913-AT-A +
3980147-T-G 4112106-T-G +
4072018-ACG-A 4203977-ACG-A +
4072019-CGG-C 4203978-CGG-C +
4397050-T-G 4529009-T-G +
4474281-AT-A 4606240-AT-A 9×T+
4760673-G-A 4892632-G-A Z20993 +
5220154-G-C 5352113-G-C +
5240124-C-T 5372083-C-T FT93749 +
5502270-AG-A 5634229-AG-A +
5588617-C-A 5720576-C-A +
5768617-A-T 5900576-A-T FT325011 +
6863782-A-C 6995741-A-C YY+
6863816-A-C 6995775-A-C B362 FT52859 YY+
7032115-C-T 7164074-C-T PH397 Y+
7311379-CTTAT-C 7443338-CTTAT-C +
8085515-TC-T 8217474-TC-T +
8479399-C-T 8611358-C-T YY18×T+
8669633-A-C 8801592-A-C Y+
8669638-T-C 8801597-T-C Y+
8791639-T-A 8923598-T-A YY+
9772265-A-T 9934656-A-T Y48472 Y+
10003200-C-A 10165591-C-A Y+
13222231-T-G 11066555-T-G +
13222255-A-G 11066579-A-G +
13242240-TC-T 11086564-TC-T +
13262946-CA-C 11107270-CA-C +
13346134-A-G 11190458-A-G +
13362513-AC-A 11206837-AC-A +
13399056-C-T 11243380-C-T +
13431666-G-T 11275990-G-T +
13431677-A-G 11276001-A-G +
13442026-T-C 11286350-T-C +
13442038-T-G 11286362-T-G +
13448645-AT-A 11292969-AT-A +
13478842-A-C 11323166-A-C +
13518802-G-A 11363126-G-A +
13518809-T-C 11363133-T-C +
13545792-C-A 11390116-C-A +
13607525-G-T 11451849-G-T FT200005 +
13830458-T-G 11709752-T-G +
14347446-G-A 12226741-G-A PH1175 YY+
14418162-AT-A +
15683653-T-A 13571773-T-A Y+
15799175-TTC-T 13687295-TTC-T +
16040819-G-T 13928939-G-T YY+
16364105-TATATATAC-T 14252225-TATATATAC-T +
16432681-C-A 14320801-C-A YY+
16651422-A-T 14539542-A-T YY+
16900856-C-T 14788976-C-T YY+
17081284-TATAA-T 14969404-TATAA-T +
17432031-TGC-T 15320151-TGC-T +
18025183-C-T 15913303-C-T BY119220 Y+
18036544-T-G 15924664-T-G YY+
18210303-C-T 16098423-C-T YY+
18640553-G-A 16528673-G-A CTS9058 YY+
18698822-A-C 16586942-A-C YY+
18966091-A-C 16854211-A-C YY+
18984974-A-T 16873094-A-T Z6478 YY+
19194972-G-A 17083092-G-A CTS9994 YY+
19371519-G-A 17259639-G-A YY+
19377304-GAGGGA-G 17265424-GAGGGA-G 6×AGGGA+
19377308-GA-G 17265428-GA-G +
19476617-A-T 17364737-A-T M4541 YY+
21096483-C-A 18934597-C-A FT314001 Y+
21146293-G-T 18984407-G-T YY+
21502798-TG-T 19340912-TG-T +
21620489-G-A 19458603-G-A YY+
22293315-T-A 20131429-T-A DYZ19 +
22458687-C-A 20296801-C-A A8030 DYZ19 +
22487716-T-A 20325830-T-A K397 DYZ19 +
23037262-T-G 20875376-T-G YY+
23498042-A-C 21336156-A-C YY+
23801731-C-CAAA 21639845-C-CAAA +
24408986-A-T 22262839-A-T +
27575928-C-T 25429781-C-T P1_Y2 +
28602525-G-T 26456378-G-T +
28628398-T-TTA 26482251-T-TTA 17×TA+
58977566-C-CATTCT 56831419-C-CATTCT +

In the table above, the meaning of the confidence field depends on whether the data comes from an FTDNA kit or an FGC kit. For FTDNA kits, + implies a "PASS" result with just one possible variant, * indicates a "PASS" but with multiple variants, ** indicates "REJECTED" with just a single variant, and *** indicates "REJECTED" with multiple possible variants. 'A*' are heterozygous variants not called by FTDNA, but still pulled from the VCF file. For FGC kits, + indicates over 99% likely genuine (95% for INDELs); * over 95% likely genuine (90% for INDELs); ** about 40% likely genuine; *** about 10% likely genuine. Manual entries read directly from a BAM file will be either + indicating positive, or * indicating that the data show a mixture of possible variants.

For the FTDNA kits, the BED data is encoded in the background color of the cells. Those cells with a white background have coverage, those with a grey background indicate no coverage in the BED file, and those with a pink background indicate the mutation is on the edge of a coverage region. These pink regions often indicate that the individual may be positive for a SNP even if there is no corresponding entry in the vcf file.

The combBED column indicates whether or not the mutation is a SNP and falls in the combBED region defined in Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data by Dmitry Adamov, Vladimir Guryanov, Sergey Karzhavin, Vladimir Tagankin, Vadim Urasin.

The McDonald BED column indicates whether or not the mutation is a SNP and falls in the BED region used by Dr. Iain McDonald in the age analysis he does for R-U106 men.

Mutation Notes:

Manual17711616-G-GA15599736-G-GA3 reads sufficiently long - all 3 show the insertion.
Manual22307726-G-A20145840-G-A2 reads - 1G and 1A.
Manual22477071-T-A20315185-T-A3 reads, all A.
Manual26286091-AT-A24139944-AT-A7 reads, 5 match the reference sequence and 2 show the deletion.
Manual22224168-A-C20062282-A-C4 reads - 3A and 1C.
Manual18872217-T-C16760337-T-C2 reads, both C.